A Postsynthetic Strategy for Oligonucleotides Containing 2-Fluoro-adenine and Isoguanine Nucleobases
Mimouna Madaoui1, Jayanta Kundu1, Dhrubajyoti Datta1
1Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States.
Organic Letters
|July 15, 2026
Summary
This study introduces a novel nonenzymatic method for synthesizing DNA, RNA, and 2'-O-methyl oligonucleotides with 2-fluoro-adenine and isoguanine. These modified nucleobases destabilize oligonucleotide duplexes, impacting their thermal stability.
Area of Science:
- Chemical Synthesis
- Nucleic Acid Chemistry
- Oligonucleotide Therapeutics
Background:
- Current methods for synthesizing modified oligonucleotides are often complex and limited.
- Incorporating non-natural nucleobases can alter oligonucleotide properties for therapeutic applications.
Purpose of the Study:
- To develop a nonenzymatic synthesis strategy for oligonucleotides containing 2-fluoro-adenine (AF) and isoguanine (iG).
- To investigate the hydrolytic conversion of AF to iG.
- To assess the thermal stability impact of AF and iG in DNA, RNA, and 2 acronym{'-O}-Me oligonucleotide duplexes.
Main Methods:
- Nonenzymatic chemical synthesis of oligonucleotides.
- Hydrolytic conversion of 2-fluoro-adenine to isoguanine.
- Thermal denaturation studies (melting temperature analysis) of modified oligonucleotide duplexes.
Main Results:
- First nonenzymatic synthesis route for oligonucleotides containing 2-fluoro-adenine.
- Successful hydrolytic conversion of 2-fluoro-adenine to isoguanine.
- Both 2-fluoro-adenine and isoguanine modifications were found to be thermally destabilizing in DNA, RNA, and 2 acronym{'-O}-Me duplexes, unlike 2,6-diaminopurine.
Conclusions:
- A novel nonenzymatic strategy enables the synthesis of oligonucleotides with 2-fluoro-adenine and isoguanine.
- These modified nucleobases exhibit destabilizing effects on oligonucleotide duplex thermal stability.
- This work provides new tools for oligonucleotide chemistry and potential therapeutic development.
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